Progressive alignment builds up a final MSA by iteratively combining pairwise alignments. It starts with the most similar pair and ends with the most distant sequence. All progressive alignment methods involve two steps: 1) build a guide tree and 2) add the sequences sequentially to the growing MSA according to the guide tree. The initial guide tree is built by neighbor-joining, where the distance matrix is calculated by the number of identical sub-sequences.
Due to its computational efficiency, progressive alignment can be applied to up to thousands of sequences. The most popular progressive alignment method has been the Clustal family developed by EMBL-EBI.The latest version is Clustal Omega. Another MSA tool for progressive alignment is MAFFT (Multiple Alignment using Fast Fourier Transform).
A list of programs implementing progressive alignment
- Clustal Omega
- MAFFT
- T-Coffee
- PSAlign